Sequence
atgc intronic sequence ATGC exonic sequencegtgagtatttgtacctcaatttcaagttctcgtgagctcacaattcttggtggcattgtcacagGCCTCCAAAGATGTGGGAAGAGCTGCAGGCTGAGATGGATCAACTATCTCCGGCCCGACTTGAAAAGGGGCCACTTTTCGCAACAGGAAGAAGAGTTGAT
Basic information
species | Selaginella moellendorffii |
transcript | EFJ38262 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ38262 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os05g04820.1 (Oryza sativa), 3'ss of exon 2
--------------------------------------------------------gtgagtatttgtacctcaatttcaagttctcg-tgagctcacaattct-----------tggtggcattgtcacagGCCTCCAAAGATGTGGGAAGAGCTGCAGGCTGAGATGGATCAACTATCTCCGGCCCGACTTGAAAAGGGGCCACTTTTCGCAACAGGAAGAAGAGTTGAT
| | || | | ||||| | || | | || |||||| ||||| ||||| |||| ||||||||||| || ||||||||||||||||| ||||| |||||||| |||| ||| | || || || || || || |||||||||| | ||
gtgagctcaaacaagtcttctgcatttcctcgtttataccagcttccgattcttctcttatctcttctccaacaattctactccctgaattggtccaaaattctaaatttcttcctggtga-attgttgcagGGCTCCAAAGATGCGGCAAGAGCTGCAGGCTGAGGTGGATAAACTATCTGAGGCCTGACCTCAAGAGAGGTGCATTCTCTCAGGAGGAAGAAGACCTCAT
upper sequence: EFJ38262 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os07g44090.3 (Oryza sativa), 3'ss of exon 1
-----------------------------------gtgagt--atttgta-cctcaatttcaagt-tctcgt--gagctcacaattcttggtggcattgtcacagGCCTCCAAAGATGTGGGAAGAGCTGCAGGCTGAGATGGATCAACTATCTCCGGCCCGACTTGAAAAGGGGCCACTTTTCGCAACAGGAAGAAGAGTTGAT
|| | ||| ||| | ||||| | | | || | || | ||||| |||| ||||| |||||| | |||||||||||||||||||||||||| ||||| ||||| ||| |||| ||| | || ||||| || || || | |||||||| | ||
ttaactgaattgagctgaaatgaacctttttaggtaggaattaattggtagtttgaatttgatatatatcattagaaattccaatttgtggttgcatt-----agGCCTTGAGAGATGTGGGAAGAGCTGCAGGCTGAGGTGGATAAACTACCTCAGGCCAGACCTCAAGAGGGGAGCATTCTCACAGGAAGAAGAAGACCTCAT
upper sequence: EFJ38262 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os07g44090.2 (Oryza sativa), 3'ss of exon 1
------------------------------------------------------------gtgagt--atttgta-cctcaatttcaagt-tctcgt--gagctcacaattcttggtggcattgtcacagGCCTCCAAAGATGTGGGAAGAGCTGCAGGCTGAGATGGATCAACTATCTCCGGCCCGACTTGAAAAGGGGCCACTTTTCGCAACAGGAAGAAGAGTTGAT
|| | ||| ||| | ||||| | | | || | || | ||||| |||| ||||| |||||| | |||||||||||||||||||||||||| ||||| ||||| ||| |||| ||| | || ||||| |
attacgaaattttcatgtcacttaattaactgaattgagctgaaatgaacctttttaggtaggaattaattggtagtttgaatttgatatatatcattagAAATTCCAATTTGTGGTTGCATT-----AGGCCTTGAGAGATGTGGGAAGAGCTGCAGGCTGAGGTGGATAAACTACCTCAGGCCAGACCTCAAGAGGGGAGCAT-------------------------
upper sequence: EFJ38262 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os01g36460.1 (Oryza sativa), 3'ss of exon 1
----------------------------gtgagtatttgtacctcaatttcaagttct-cgtgagct-cacaattcttggtg--gcattgtc----acagGCCTCCAAAGATGTGGGAAGAGCTGCAGGCTGAGATGGATCAACTATCTCCGGCCCGACTTGAAAAGGGGCCACTTTTCGCAACAGGAAGAAGAGTTGAT
| | |||||| |||| | || | |||| | ||| || || | ||| ||||| | | || ||||| ||||| ||||||||||||||||||||||| || |||| || | || || ||| ||| || || ||||| || ||| | ||
tgtttatatcgtaatttagttgctatacctctctctttgtatctcactctctgacagtgtgtgaataatataatgtgtgttgctgagttgctgtgtacagGATTGGAGAGGTGTGGCAAGAGTTGCAGGCTGAGATGGATCAACTACCTGAGGCCTGATCTCAAGAGAGGCAGCTTCTCCCAGCAGGAGGAGGAGCTCAT
upper sequence: EFJ38262 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os01g18240.1 (Oryza sativa), 3'ss of exon 1
----------------------------------------------gtgagtatttgtacctcaat---ttcaagt-tctcgtgagctcacaattcttggtggcattgtcacagGCCTCCAAAGATGTGGGAAGAGCTGCAGGCTGAGATGGATCAACTATCTCCGGCCCGACTTGAAAAGGGGCCACTTTTCGCAACAGGAAGAAGAGTTGAT
|| || || |||| | ||||||| || | ||| || | | | ||||| |||| || || |||||||| || |||||||||||||||||||| ||||| | |||| ||| | || || || || || || ||||||| || | ||
gtgagcatcaaaatattctgcactttattcttgtcgattatccactttgtgttctttcttctcagtcaattcaagtctcccctgaaatcttagcaatcaaacgaattgttgcagGGCTTCAGAGATGTGGCAAAAGCTGCAGGCTGAGATGGATAAACTACTTGAGGCCTGACCTAAAGAGAGGTGCATTCTCTCAGGAGGAAGAGGACCTCAT
upper sequence: EFJ38262 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G150841_T02 (Zea mays), 3'ss of exon 1
-----------------------------------gtgagtatttgtacctcaatttcaagttctcgtgagctcacaattcttggtggcat-tgtcacagGCCTCCAAAGATGTGGGAAGAGCTGCAGGCTGAGATGGATCAACTATCTCCGGCCCGACTTGAAAAGGGGCCACTTTTCGCAACAGGAAGAAGAGTTGAT
|| ||| || || | | | | | | | | || | || | || ||| || | || ||||||||||||||||||||||| ||||||||||| ||| |||| ||| | || ||||| || ||||| | || || || | ||
ttgcattggttgctagcagtcgcagagttgaattgatggcaattcgttaatcgttatggtgatgatgctgtttatttttgcatgcttgcgtgtgcattagGTCTAGAGAGGTGTGGGAAGAGCTGCAGGCTGAGGTGGATCAACTACCTCAGGCCGGACCTCAAGAGGGGAGCGTTCTCGCAGGAAGAGGAGGACCTCAT
upper sequence: EFJ38262 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G064744_T01 (Zea mays), 3'ss of exon 1
-----------------------------------------------------------------------------------------------------------gtgagtatt-tgtacctcaatttcaagttctcgtgagctcacaattcttggtggcattgtca--cagGCCTCCAAAGATGTGGGAAGAGCTGCAGGCTGAGATGGATCAACTATCTCCGGCCCGACTTGAAAAGGGGCCACTTTTCGCAACAGGAAGAAGAGTTGAT
| | ||| || | || || | | | || | || || ||| ||| | |||| | | ||||| || ||||||||||||||||||||||||||||| || ||||| ||| | || |||||| ||| || || ||||| || || | ||
gtacgagtacgacccatgatttgtaatgtaaaaagggttcgtcagaaataatatatataaacgctgcgttaatttgcttgatatttgatctcctgctagctgttgccttttgcattgtgatcgtcgatattatttagtcagagaatgttttttttttgtgtgtgtgtaagtaagGCTTGGAGAGATGCGGCAAGAGCTGCAGGCTGAGATGGATCAACTACCTGCGGCCTGACCTCAAGAGGGGCAGCTTCTCCCAGCAGGAGGAGGATCTCAT
upper sequence: EFJ38262 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G496770_T01 (Zea mays), 3'ss of exon 1
---------------------------------------------------------------------gtgagtatttg-tacctcaatttcaagttctcgtgagctcac-aattcttggtggcattgtcacagGCCTCCAAAGATGTGGGAAGAGCTGCAGGCTGAGATGGATCAACTATCTCCGGCCCGACTTGAAAAGGGGCCACTTTTCGCAACAGGAAGAAGAGTTGAT
||| || || | | | | || ||| | || | |||||| | ||| | | |||| ||||| | || ||||||||||||||| | ||||||||||| |||||||| | | |||| ||| ||| || | |||| || ||| | |
gtaagacgaccagcgattcattcgccgccgccgccgctgcatgcgcctcaaaactgatcgtagacaagtgtgcgtgcatgatgcattgggtatgggt-ctcaaaaactgaggaattctgtgcggcgtcg--gcagGGCTCCAGCGGAACGGCAAGAGCTGCAGGCTGCGGTGGATCAACTACCTCCGGCCGGGCCTGAAGCACGGCACCTTCTCCCCGGAGGAGGAGGAGACGGT
upper sequence: EFJ38262 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G147698_T01 (Zea mays), 3'ss of exon 1
-------------------------------------------------------------------------------------------gtgagtatt----tgtacctcaatttcaagttctcgtgagctcacaattcttggtggcattgtcacagGCCTCCAAAGATGTGGGAAGAGCTGCAGGCTGAGATGGATCAACTATCTCCGGCCCGACTTGAAAAGGGGCCACTTTTCGCAACAGGAAGAAGAGTTGAT
|| || | || | | | | | | |||| || | || | ||| |||||||| | || ||||| ||||||||||||||||| ||||| ||||| || |||| ||| | || |||||| || |||||| |||| || || | ||
gtatattatatctcacttgctttttgcacgtatacatacatgcgcgcccagaattaccagcaacaagctcatgaaaaagcagcagcagaatgtaagctgtggcgtgcattacggtgttacttggctagtagctaacc-tgtttcttcatgctgtt-cagGCCTCGACAGGTGTGGCAAGAGCTGCAGGCTGAGGTGGATAAACTACCTGAGGCCAGACCTCAAGAGGGGCACATTCTCGCAAGAGGAGGAGGACCTCAT
upper sequence: EFJ38262 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA17G09310.1 (Glycine max), 3'ss of exon 1
------------------gtgagtatttgtacctca--atttcaagtt-------ctcgtgag-----ctcacaattc--ttggtggcattgtcacagGCCTCCAAAGATGTGGGAAGAGCTGCAGGCTGAGATGGATCAACTATCTCCGGCCCGACTTGAAAAGGGGCCACTTTTCGCAACAGGAAGAAGAGTTGAT
| | | || | || | ||||| | | ||| || || || | ||| | |||| || ||||||||||| ||||| |||||| |||||||||| |||||| | |||| || || || || ||| || || || | || || || | ||
gtaacaacttgtatattcttaatttcttctcttccattacttcaaacgaaaaaaacatgggagagagcttcttaactcattccatggtgaatttgcagGACTGCAAAGATGTGGAAAGAGTTGCAGGTTGAGATGGATAAACTATTTGAGGCCTGATTTAAAGAGAGGCATGTTCTCACAGAAAGAGGAGGATCTAAT
upper sequence: EFJ38262 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA05G02550.1 (Glycine max), 3'ss of exon 1
------------gtgagtatttgtacctc---aatttcaagttctcgtgag-----ctcacaattc--ttggtggcattgtcacagGCCTCCAAAGATGTGGGAAGAGCTGCAGGCTGAGATGGATCAACTATCTCCGGCCCGACTTGAAAAGGGGCCACTTTTCGCAACAGGAAGAAGAGTTGAT
| | || | || ||| || | | ||| || || || || || | |||| | ||||||||||| ||||| |||||| |||||||||| |||||| | |||| || || || || ||| || || || ||||| || || | ||
gtataacaacttacaacttttcttctctttcaaatgaaaaaaacatgggagagagcttcttaactcatttcatgatgaatttgcagGATTGCAAAGATGTGGAAAGAGTTGCAGGTTGAGATGGATAAACTATTTGAGGCCTGATTTAAAGAGAGGCATGTTCTCACAGCAGGAGGAGGATCTTAT
upper sequence: EFJ38262 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA10G28250.1 (Glycine max), 3'ss of exon 1
-------------------------------------------------------------gtgagtatt-tgtacctcaatttcaagttctcgtgagctcacaattcttggtggca-ttgtca--------cagGCCTCCAAAGATGTGGGAAGAGCTGCAGGCTGAGATGGATCAACTATCTCCGGCCCGACTTGAAAAGGGGCCACTTTTCGCAACAGGAAGAAGAGTTGAT
||| | | || | ||||| || | | ||| |||| | | |||| | |||| | || ||||||||||||||||||||| |||| ||||| || ||||| |||| || ||||| || || || || || || ||||| | ||||
gtatatacatacatagtactatatataataatgtttgtttcaacacttcattgatgttgtagtgtgcacaatgaagtacaattcaaaacacaagagagtctttaatttctaaccttaattgtaaacacatgccagGTTTGCAGAGATGTGGGAAGAGCTGCAGGTTGAGGTGGATAAATTATCTAAGGCCTGATTTGAAGAGAGGAGCATTCTCACAGCAAGAAGAGAACATGAT
upper sequence: EFJ38262 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: Vv14s0060g00240.t01 (Vitis vinifera), 3'ss of exon 1
---------------------------------------------------gtgagtatttgtacctcaatttc-aagttctcgtgagctcacaattcttggtggcattgtca-cagGCCTCCAAAGATGTGGGAAGAGCTGCAGGCTGAGATGGATCAACTATCTCCGGCCCGACTTGAAAAGGGGCCACTTTTCGCAACAGGAAGAAGAGTTGAT
|||| ||| | | ||| | | || |||| | ||| | |||| | || || |||||||||||||||||||| |||||||| ||||| | |||| || ||||| ||||| || || ||||||||||| ||||
gtacccatgtatgttcatcttttggtgtgtcactgtaaatgcagaacagcaaccgttattgagaccaagtctcctgtgttttttttttcttttttctctttctatcataattggcagGTTTGCAGAGGTGTGGGAAGAGCTGCAGGCTAAGATGGATTAACTACTTGAGGCCTGATTTGAAGAGGGGAGCATTCTCACAACAGGAAGAGAGCCTGAT
upper sequence: EFJ38262 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------------------------gtgagtatttgtacctcaatttcaagttctcgtgagctcacaattct--tggtggc--attgtcacagGCCTCCAAAGATGTGGGAAGAGCTGCAGGCTGAGATGGATCAACTATCTCCGGCCCGACTTGAAA-AGGGGCCACTTTTCGCAACAGGAAGAAGAGTTGAT
|| || | ||| | | || | | | | || | | ||| || ||||| || ||||| ||||||||||||||||||||| ||||||||||||| | | || || |||||| ||| | | | ||| |||| ||||| |||||
aatgaaaatggtttcgcaggaatgaagagcgaccaggttagcacactttgttttgtactaatcactaaccaatatttgtgtttgtgaatggatgcaacagGTCTTCAAAGGTGTGGGAAGAGCTGCAGGCTGCGATGGATCAACTACTTGAGACCAGATTTGAAACGAGGGGTATTCTCCGCGACAG-AAGAAAGTTTGAT
upper sequence: EFJ38262 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S277_14V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------------------------------gtgagtatttgtacctcaatttcaagttctcgtgagctcacaattcttggtggcattgtcacagGCCTCCAAAGATGTGGGAAGAGCTGCAGGCTGAGATGGATCAACTATCTCCGGCCCGACTTGAAAAGGGGCCACTTTTCGCAACAGGAAGAAGAGTTGAT
|| || | | | | || || | | || || || || ||||| |||||||| || ||||||||||||||| || | ||||||||||| |||||||| || |||||| | ||| |||||| | || || | |||||
taacatatttaaagtgaaaaaaggttcttttcattgatgtaaggaatctaatcgtgtggagaaattgatgaatgttcctggacaatgaatgc--tgcaacagGTCTCCAAAGGTGCGGGAAGAGCTGCAGGTTGCGGTGGATCAACTACCTCCGGCCGGATTTGAAACGAGGCGTATTTTCGGCAGCAGAGGAGAACTTGATMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|169063248|gb|FE472706.1|FE472706EST: CATTACAAAGTATGGCCACAAATGCTGGAGCATCGTACCGAAACACGCAG GCCTCCAAAGATGTGGGAAGAGCTGCAGGCTGAGATGGATCAACTATCTCC
genomic: CATTACAAAGTATGGCCACAAATGCTGGAGCATCGTACCGAAACACGCAGgtgagtattt ... attgtcacagGCCTCCAAAGATGTGGGAAGAGCTGCAGGCTGAGATGGATCAACTATCTCC
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
27 (upstream exon),
35 (downstream exon)
Score:
6CTTCGCAAAGGACTGTGGTCTCCAGAGGAAGATGAGAAATTGGTGAGGTACATTACAAAGTATGGCCACAAATGCTGGAGCATCGTACCGAAACACGCAGgtgagtattt ... attgtcacagGCCTCCAAAGATGTGGGAAGAGCTGCAGGCTGAGATGGATCAACTATCTCCGGCCCGACTTGAAAAGGGGCCACTTTTCGCAACAGGAAGAAGAGTTGAT
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtacctcaatttcaagttctcgtgagctcacaattcttggtggcattgtcacagGCCTCCAAAGATGTGGGAAGAGCTGCAGGCTGAGATGGATCAACTATCTCCGGCCCGACTTGAAAAGGGGCCACTTTTCGCAACAGGAAGAAGAGTTGAT
agctcac putative branch site (score: 6)
aatttcaa TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtatttgtacctcaatttcaagttctcgtgagctcacaattcttggtggcattgtcacagGCCTCCAAAGATGTGGGAAGAGCTGCAGGCTGAGATGGATCAACTATCTCCGGCCCGACTTGAAAAGGGGCCACTTTTCGCAACAGGAAGAAGAGTTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG